New York state Comptroller Thomas DiNapoli’s latest audit suggested the Metropolitan Transportation Authority gave Apple an unfair advantage last year when the company bid for a spot in Grand Central Terminal.

A fresh audit by state Comptroller Thomas DiNapoli says the MTA last May allowed the California-based tech giant to set a daunting hurdle for rival bidders to clear in a tight, 30-day window — namely, that they be willing to front $5 million in cash.

“The competitive process followed by MTA . . . was at a minimum severely slanted toward Apple,” reads the report, submitted to MTA officials Friday and expected to be made public today.

DiNapoli’s report notes that Apple had been in private talks with the MTA for more than two years leading up to the bidding process.

In a saucy move that was rejected by the MTA, Apple even tried to get reimbursed by taxpayers for the initial $2 million it had paid the restaurant Metrazur to vacate the balcony atop the historic commuter hub, the report found — a deal that ultimately was worth $5 million.

MTA Chairman and CEO Joseph Lhota told The New York Post that DiNapoli’s report is overtly “bias against the MTA and Apple,” and he said the audit is “not fact-based, and, accordingly, their opinion is worthless.”

“The MTA’s lease process with Apple was open, transparent and followed both the spirit and letter of the law,” Lhota contended.

Apple opened its doors in Grand Central’s last winter and pays $1.1 million in rent for 2012, which the audit noted is below market, and the company notably does not share a percentage of its sales with the MTA. It is the only retailer at the station with such a deal.

On the plus side, there is an awesome Apple Store with free Wi-Fi in Grand Central Station!